Genesis of Evangelion
by RyoshiMorino
Summary: Direct Sequel of Rebirth. With Shinji absorbed into Unit-01, Asuka and the others must find a way to cope with his absence while the threat of the Angels begins to grow as Seele puts their plans into motion. With the battle raging on, will Shinji be able to aid his friends, or watch the world burn?
1. Chapter 1

**_Rebirth: Part Two_**

 ** _Genesis of Evangelion_**

 ** _1:Funeral Rights_**

* * *

As some things often change, some things will always remain the same. Why? Because that was the way of the world, and very few beings could change it. And the way of the world as it was now was nothing short of hell if you were to ask Asuka Langely Shikinami.

It had been three weeks since the Fifteenth Angel had descended upon Tokyo-03, and three weeks since she had watched her fiancee disappear into his Evangelion. She had stayed strong for the rest of her team, and herself for that matter, but the fact of the matter was that there was only so much she could take.

School was one thing she had to deal with.

Every student knew of Shinji Ikari's involvement with the Evangelions, and, by default, the entire squad. It was also well-known that she and Shinji had been deeply involved, just not how deeply. Rumors had started almost immediately as soon as she landed in Tokyo-03 nearly eight months ago about the pair, and those rumors soon proved the fiery ginger right.

It didn't take much to convince her of Shinji's feelings for her, not much at all, given that he practically told her the first time that they kissed. His actions spoke louder than his words ever could. Risking his life for her, and taking unnecessary risks for the team as he did made it clear that the young man cared more for his fellow pilots than he did himself.

But in the end, it hadn't been enough for her to keep him with her. To her, he had made the ultimate sacrifice for his mother, whom had been trapped inside Unit-01 from the beginning, just like her own mother.

Asuka sighed as she walked through the halls of the school, trying to ignore the looks and whispers she was garnering. Really, what was there to look at? She knew she was good looking enough for most boys, and she hadn't done anything with her hair in a while, it still hung loose around her shoulders in red waves. So what the hell were they gawking at?

"Hey, isn't she the one that - "

"Yeah, her boyfriend, I hear," a pair of girls whispered, causing a pang in Asuka's chest. Even though she knew that Shinji wasn't really gone, Commander Ikari had made it seem that he was in order to keep Unit-01 and Yui Ikari safe from Seele. Mana Kirishima had explained long ago that Seele had ruthlessly taken her own mother as a hostage in order to make the prospective pilot do their bidding as a spy within the pilot ranks.

It was a plot that had nearly gotten herself, Shinji and Ryoji Kaji killed. But to that end, Mana had ultimately failed because Seele had already forced her mother's soul out of her, and into a new Evangelion that was soon to arrive in Japan.

But within the three weeks since Liliel's assault, and Shinji's disappearance into Unit-01, there had been no sign another Angel attack on the horizon.

"I heard he was killed in that last attack," whispered the first girl, "Not by the monsters, but by his own team!"

"No! Really?"

Asuka ground her teeth.

"Yeah, yeah, Maki told me she saw the whole thing from the hillside," the girl said, "His robot had gone crazy, or something so they really didn't have a choice but to kill it." She said, "I hear it attacked Asuka's machine, and nearly killed her if the others hadn't pulled it off of her!"

"Poor Asuka," the second girl said, "It's too bad, they really looked nice together."

"Yeah, I hear they were gonna get married as soon as this was all over," the first girl said sadly, making Asuka's eyes sting as she passed right by them.

 _It doesn't matter,_ she told herself, _He's not dead._ _The funeral is just for show._ She growled as she recalled the mock funeral the Commander was arranging for his son. She knew why he was doing it. If Seele got wind of Yui being outside of Unit-01, then they'd most likely kill her before anyone could blink, And Shinji was their ace pilot.

Unit-01 was still heavily damaged, even though it was seen to be repairing itself faster than normal, the bio-mechanical machine would be out of commission for some time. And since Shinji was no longer around, it would do well for those that admired him around school to _mourn_ him. To Asuka, it was just a smoke and mirror act.

Shinji was coming back, and she knew that he would, even if she had to drag him out of that damned machine-monster herself.

As she made her way to class, she spotted her fellow pilots waiting outside the classroom for her. The six people were as quiet as they usually were as of late, but they all had a smile on their faces as they greeted her. Her friends, Hikari Horaki, Mana Kirishima, and Mari Makinami were the best of her support in there ranks, the only other girl being Rei Ayanami, Shinji's half-sister.

Asuka liked her well enough, but the girl was more than a little emotionally stunted. Her boyfriend, and designated Sixth Child, Kensuke Aida was helping her with that on some levels, the two of them being lovers and all, but the girl was still only just coming out of her shell because of her brother's disappearance. Yui had helped her with some of it. The woman doted on the girl every chance she got, and adored her as if she'd raised her.

Another couple within their group was the Seventh Child, Touji Suzuhara, and the Ninth, Hikari Horaki. Even before becoming pilots, the two had been hot for each other, they just needed the right push. And becoming an Eva pilot had made Hikari worry for Touji more than ever, and from that point on, they were inseparable. Not long after that, Hikari had been selected for becoming a pilot herself, and had helped in taking down the rogue Evangelion Unit-01.

"Morning, Red," Mari smiled at her, "Ready for another fun-filled day in class?"

"Nope," Asuka laughed.

"Good, cause there's nothing fun about this place," the girl deadpanned, causing her to laugh more as she moved into the classroom. "Seriously, how many times a week can we listen to the same damned lecture over and over again?"

"Who knows?" Touji sighed, moving to his seat, "But at least any assignments we get in this class are easy. Rinse and repeat, right?"

"Yeah," Mana nodded, smiling for a moment before she turned and saw the chalk board. "Oh..."

Asuka turned and felt her heart clench painfully in her chest. It was meant as a reminder of the funeral that was to take place soon, but it still made her angry to think that Shinji would soon be forgotten as if he'd never existed. Heroes came and went, and when they went, no one remembered them save for the texts in History books.

She wouldn't let that happen, that much she knew. But those words written on the board pushed her over the edge. "I need to go," she whipped around and rushed out the door.

"Asuka!" Hikari yelped, chasing after her.

She ran down the hall to the nearest bathroom, and shut herself in the first stall she could find. She sank to the floor, drawing her legs up against her chest, and burying her face in her skirt.

"Asuka," Hikari's voice drifted to her ears, "Look, I know it's bad, but - "

"He's not dead," the red-head said, her voice shaking, "I know that, and you know that...but why is it that every time I turn around, I get hit with the same line of shit?!"

Hikari sighed from the other side of the door, "The commander means well, you know that."

"I don't give a damn!" Asuka snapped, "He's alive, dammit, but if everyone keeps telling me he's not...I'll start..." Her body shook as sheraised her head up to look down at the ring on her finger, "The only picture of him I have is that night at the Christmas party." She smiled at the memory, "I'm scared...I might start forgetting him, Hikari..."

Hikari slammed her palm against the stall door, "Don't say that!" Hikari snapped angrily, "Don't you dare say that after everything that's happened!" She cried, "I knew him less than you did until I got involved with all of this madness, but I know I'll never, ever forget him! I'm alive because of him in so many ways!"

"So was I," Asuka muttered.

"Asuka - "

"No, you don't understand," Asuka went on, shaking her head, "For the longest time, I was trained to be an Eva pilot, they even chose who my father was going to be from donors, nothing but the best and the brightest. When I came out, it was all one big schooling until I was just as smart, athletic, and martially capable as possible before I was placed inside Unit-02. It was the only thing I lived for." She admited sadly, "And I met Shinji, and the rest of you...and I had friends for the first time in my life...and I fell in love, really fell in love, not like that silly crush I had on Kaji...he made me feel...incredible!" She leaned her head back against the door, smiling as tears fell from her eyes, "I'd never felt so wanted before in my entire life. He was everything I wanted to be in a pilot, and more than I could have dreamed of as a...a partner...and now he's..."

"He's just sleeping," Hikari pointed out, smiling even though her friend couldn't see her, "He'll be back, and we all know that...just stop listening to all of those idiots that want the world to believe he's dead. It doesn't matter, because we know the truth."

"But what if he doesn't come back?"

"He will!" Hikari said loudly, "Just don't lose hope."

The door opened slowly, revealing Asuka, her eyes red and her cheeks flushed, smiling sadly at her friend, "All I've ever had is hope...but what if that isn't enough?"

"Then we'll just have to make something happen, won't we?" Hikari smiled and brought the girl into her arms, "Don't forget, you're not the only one that misses him. We all do in our own way. You lost your fiancee, Rei lost her brother, and we all lost a friend."

"I know," Asuka said against her shoulder, "But why do I have to keep remembering all of this pain?"

Hikari shook her head, "If there was no pain, then whatever you felt for him wouldn't have been real at all," she told the girl, "That's life. For what we want most, we have to endure some of the worst pains imaginable, but in the end, it'll all be worth it."

Asuka was quiet for a moment, contemplating what she would, or could say to her friend before her own words rang out in her head, "I won't stop trying to get him back," she repeated, smiling as she remembered the core of Unit-01 warming to her touch. "And...I don't think he'll stop trying to come back, either."

"I'm sure he won't," Hikari said, smiling a little at her friend, "Now come on, we should get back to class."

Asuka shook her head, "Sorry, but...I think I'm gonna ditch today...I'll call Misato and let her know, alright?"

Hikari rolled her eyes, and sighed, "Alright, but don't make it a habit, okay?" She said, dropping into her Mother Hen Mode, "I know you've already finished college and all that, but you do need the experience of a proper school life."

"Boring lectures on Second Impact, and homework I could do in my sleep," Asuka smirked, and let her go, "I'll see you later, Hikari."

=x=

"How are the repairs coming?" Gendo asked as he stared up at the silent Unit-01. "The hole from Unit-00's rifle seems to have healed up, but why are we not checking the systems for any signs of contamination?"

Ritsuko sighed, "It's not that we aren't doing it, Commander, it's because we can't." The blonde said, grimacing at her charts, "We've been at this for nearly three weeks now, and we're still locked out of the system. I don't know whether or no if Shinji's blocking us, or if it's the Eva itself, but we just can't get a reading from either one of them."

Gendo sighed, nodding, "I was half expecting this. From what you've told me after his escape from the Fifteenth Angel, Unit-01 went fully berserk in its released state." He said, looking at the Evangelion, its new armor in place. "Add to the fact that it managed to devour two S2 engines, and we had the makings for a calamity. I don't know what pushed Shinji to such a state to lose control as he did, but even he must have had his limits."

"Hasn't Yui told you anything?" She asked curiously, "I would have thought she would know what happened while they were joined inside the core?"

"She's rather enigmatic about it," he sighed, smirking, "I can't say that I blame her, but it is frustrating. All that she would tell me, though, was that whatever happened while he was trapped in the Sea of Dirac was that Shinji was beyond furious."

Ritsuko nodded, "He pushed the negative rage too far, and ended up pushing Yui out of Unit-01 so he could take her place before she was destroyed because of his own anger." She said thoughtfully, "It's lucky for her that she was pushed out of the core the way she was. She may have been destroyed if she'd shared it with Shinji for much longer than she did."

"It is fortunate," Gendo smiled, "Though she won't tell me what all went on, I'm...happy to have her back...erm, what are we doing about Unit-01's pilot?"

Ritsukoe looked at the man for a moment before sighing, "If you're asking what I think you are, I think it'd be a bad idea for one of the others to pilot it." She said, taking out and lighting a cigarette, "Though he knows them well, Shinji's soul was filled with rage at the moment of absorbtion, which means Unit-01 could react much the same way Unit-00 did when it first encountered Rei."

"Asuka could pilot it," Gendo pointed out, looking up at the purple behemoth, "Matter of fact, I believe she may be able to make contact with him."

The woman nearly dropped her cigarette upon hearing this, "Are you suggesting we place Asuka inside Unit-01?" She asked incredulously, "Are you out of your mind?!" Gendo winced as the woman snapped at him, "Not only could that not work, but think of the mental strain it would place on that girl! What if she breaks down? What if she does make contact and Shinji reacts violently?" She pointed out, "She could easily be absorbed as well!"

"It's still worth a shot, and I wouldn't dare put her in the entry plug unless she wanted to go." Gendo said, trying to calm the woman, "We can rig up an external means of communications, the video lines should be enough to get a message across."

"She sat beside this Eva for hours, and nothing happened." Ritsuko pointed out. "What makes you think he'll respond?"

"Because we'll use a Dummy Plug to ensure he's awake," Gendo sighed, distaste entering his voice. Shinji had already told him about the Dummy Plug system, but knew that right now it was more than needed if they were to retrieve him.

The blonde doctor sighed before taking a long drag from her cigarette, "I've actually grown fond of those kids...you haven't done any testing on Rei for a while now, and she's developing into quite a good young woman," she said, "Her relationship with the other pilots seems to be a good thing in the long run. Her sync rates are higher than they've ever been, and she's much more social, even if it's just within that group."

"Her relationship with Pilot Aida is more of a concern to me," Gendo said, sighing as he rubbed the bridge of his nose, "I never would have thought she'd actually fall in love with someone, let alone such an odd young man."

"Young man, not boy?" Ritsuko asked, smirking.

"If he is able to make her happy, then he has my blessings," Gendo grumbled, "I am not the girl's father, but Yui seems to approve of the match, and Rei is quite attached to him. He is a good man, jokes aside."

Ritsuko hummed in thought for a moment, looking at the Evangelion laying dormant in front of her, "Are you sure you want to go through with this?"

"What choice do we have?" Gendo asked, "Shinji was our best pilot, even better than Asuka, I'm sorry to admit, and he kept them all together. Without him, I've seen quite a decline in the sync rates all around, Asuka's being the most prominent...this needs to be done, or else she won't be able to pilot Unit-02 anymore, let alone UNit-01."

"Germany would replace her," Ritsuko nodded in understanding. "Given they were engaged, I can't say I like the fact that she would be forcibly removed from Japan to make room for the new pilot."

"Which is why this needs to be done." Gendo sighed, turning toward the hall, "I will leave the date up to you, Doctor Akagi. In the meantime, I have a funeral to arrange."

Ritsuko shook her head, "Burying your own son before he's actually confirmed dead? What kind of mad world do we live in?"

"A world of monsters and men," Gendo said as the door opened for him, "And it's hard to tell the difference at the best of times."

=x=

 _There was so much damage, yet he knew that he had to repair if before anything could be done. The Evangelion wanted this as well. It was incomplete to a dangerous fault. It wanted more strength to fight with._

 _He was only too happy to oblige the being as his soul spread through the titanic form of the Evangelion, strengthening and repairing where it was needed. It would take months for him to totally raise Unit-01 to what it wished to be, and what he needed it to be._

 _Even though he could split off and return at any given time, he had little choice given what was to come. The Angels would attack with full force as soon as he was released from Unit-01, and there was so much to do even before that._

 _Bardiel was coming, and was stronger than ever thanks to the advanced Unit-13. Given Abraham's intelligence, he was in for the fight of his life against the beast when it broke loose from NERV's control. And then he would have to face the Angel that had pushed him passed his breaking point and prompted him to nearly become an Angel himself._

 _He knew that Zuriel would be ten times stronger given what he had seen already from the lesser Angels. He had to be ready for him. He would not allow his team and loved ones to be harmed by the monstrous creature that would blast its way into the Geo-Front, and nearly kill Asuka and Rei._

 _He would destroy him long before he let him touch them. He would rip him to pieces!_

Unit-01's shone bright blue for a moment as Ritsuko took notice. A small spike of fear rushed through as those eyes went dim once more. The Eva was now able to operate without an umbilical cable, making the bio-mech a loose canon should Shinji's emotions run wild. The sync test would prove whether or not it would go berserk, but the price would either be a cooperative machine, or a berserk monster that would ultimately have to be destroyed if it went wild.

"Please," she said mostly to herself, but spoke up to the Evangelion itself, "Please don't let them feel that pain of losing you again."

=x=

It felt strange to her, burying an empty casket in the Geo-Front alongside Mayumi's grave. Even though she knew that he wasn't dead, and that they weren't actually burying him, Asuka couldn't keep her hands from clenching into the fabric of her black uniform. All of the pilots were dressed in their NERV attire, looking prim and proper.

It was all Asuka could do to keep herself from ripping the garments off, and leaving the farce behind. But the fact remained that there was one Seele Chairman in attendance. The man had demanded to see the body, but strangely, Gendo had convinced him that his son was in no condition to be seen. Asuka found herself reaching for the empty holster at her side, wishing she could shoot the man for what he and his fellows had done to Mana, and her mother.

But it wouldn't do for her to become a murderer...yet.

Mana wasn't in attendance for obvious reasons, those being the fact that she was no longer working for Seele and, therefore, a loose end that they would ultimately wish to tie up. Yui was there, but the woman's face was covered by a black veil that obscured her face completely as Gendo spoke over his son's grave.

On her finger, Asuka wore her engagement ring in full display as a six gun salute was fired off and the pilots paid their respects to their captain. Rei sidled up to the red-head and gripped her hand tightly, "I know that this is not what it seems...but it hurts," the girl said, "I'm not sure why, but it hurts worse than when we lost Mayumi."

Asuka gave the girl a small smile, and wrapped her arm around her loosely, "Hey, don't worry about it, Wonder Girl, this is all just for show," she whispered, hoping no one would overhear her. "He's coming back, just like Hikari and Yui said. He wouldn't leave us like this."

"I know that, but...he's my brother..." Rei muttered quietly, "He was the only family I had for so long."

Asuka gave her shoulders a small squeeze, "Now you have your mama. And me, too." Rei looked at her strangely, and the girl sighed, smiling, "Well, since we were getting married, that would make us sisters, right?"

Rei looked surprised for a moment, then a genuine smile came to her face, "I...suppose that would be true..."

"Right, so that makes you and me family," Asuka said in a sing-song voice just loud enough for her to hear. "And you have Kensuke, and the rest of us to count on, so you really don't need to be so glum. He'll be back, and we'll all be waiting on him."

"We will not lose another pilot," Rei said with conviction.

"Damned right!"

* * *

 _ **This is the beginning of the Epic Finale of Evangelion Rebirth! The Poll kinda got snowballed since out of the 700+ readers, only 43 voted, which led to a point of being split off into a seperate sequel. Now, as we see here, things are looking grey for the the pilots as even Asuka begins to feel Shinji's absence, and Gendo decides to set up a sync test for Unit-01 and Asuke herself.**_

 _ **Seele's plans for Instrumentality have not gone unchanged, and with the help of Angels on both sides of the board, how will the pilots deal with these threats?**_

 _ **Find out by reading Genesis of Evangelion!**_

 _ **Don't forget to review!**_


	2. Chapter 2

**_Genesis of Evangelion_**

 ** _2: Ghost in the Machine_**

* * *

The funeral for Captain Shinji Ikari was one that was short, and tearful for many that knew of him. As the pilots returned home for the evening, Asuka led Rei to her room, and put the girl to bed for a time until she could have dinner ready. Kensuke was right behind her, and stayed to watch over her until then.

Upon discovering Rei and Kensuke's rather sordid relationship, Yui had nearly flipped out, along with Misato. Even though she now knew that Asuka and Shinji had been lovers, she hadn't realized the second couple had been engaged in a physical relationship for far longer. What was more, the rest of the pilots knew about it, and she didn't!

Case in point, it was damned near impossible to try and stop Rei from sneaking into her boyfriend's room. To anyone with a pair of eyes, it was easy to see that the two were inseparable. As Asuka left the two, she couldn't help but feel a spike of jealousy for the recent lack of warmth in her own life. Still, she couldn't deny that the two were lucky.

Hell, she thought that they were all lucky for being alive so far. What with the Angel's, Seele, and rogue Evangelions to worry about. As she walked out into the hall, she found herself wondering if her own Eva would suffer the same fate as Unit-01. Unit-02 was the final production model, but that didn't mean it was perfect. As far as she could tell, hers and Shinji's weren't all that different from one another, save for the color of their armor.

When she made it back to the main area, it was to find Touji and Hikari on the couch together as usual with little Sakura in between them. She felt for the little girl, seeing as she had a bit of a schoolgirl crush on Shinji for being her savior during his first battle. The little dear was distraught when she heard that Shinji was gone, and it nearly tore her brother apart seeing the her so upset.

She was now staying with them under Touji and Hikari's supervision, the two of them equally as protective of her. Yui was just as much a mother hen as Hikari was when it came to all of them, however, especially herself and Rei. Having heard of her engagement to her son, Asuka was now her third favorite person. First being Shinji, and second being Rei...Shinji was older...sort of.

Currently, she and Misato were sitting at the table discussing her upcoming wedding, which still tended to blow the German ginger's mind when she thought about it. Misato did not seem to be the marrying type, yet here she was looking through catalogs full of wedding dresses and other such things. It was a better topic than the funeral.

"Yui, I get that it's a special thing, but I don't think something like this...parachute is what I'd want to wear!" Misato grumbled, taking in the size of the dress on the page. Asuka peeked over her shoulder at it and nearly burst of laughing. It was a normal dress from the waist up, but the bottom half did indeed look like a miniature parachute. The thought of the major in something so ridiculous was hilarious.

"Oh, but dear, you'd look incredible in this!" Yui gushed, "A dress like this would have been all the rage before I married."

"That was what? Sixteen years ago?" Mari put in her two cents, looking down at the dresses, "Something like this one would be the more modern type of dress for weddings." She said, pointing out a simple white gown with slit up the left side that showed off the model's legs, while the rest of it went down to the ankles, "And she'd look really good in it."

"Can't I just wear my uniform?" Misato moaned when she saw some of the prices on the dresses they were scoping out.

"No," was the resounding answer from her tormentors.

Asuka reached out an patted her on the shoulder for support, "Cheer up, at least you're actually gonna get your guy." She said, and went about getting dinner started. Misato looked at the girl a little sadly, but smiled her thanks.

"You'll get yours, too, Asuka," Misato put in, "It's not like we're going to stop trying to get him back. Ritsuko's even going to set up a sync test so we could maybe get in touch with him, and find out if he can come back on his own."

Asuka looked back at her, "Who would they use?" She asked, looking at the other woman in the room, "Yui can't sync with an Eva."

"It's gonna have to be you, Asuka," Yui sighed, shaking her head, much to the girl's shock, "You were the closest to him aside from Rei, but your relationship with him would probably give you the most chance to get him to respond."

Asuka's face turned from shock, to anger within seconds, "Absolutely not! I'm not going into that entry plug for that monster!"

"You won't have to," Misato said, trying to soothe her, "We have a system in place called a Dummy Plug to act as your stand-in while we start a communications link from HQ. If anything goes wrong, you and the others will be well away from Unit-01 if things turn sour. The only problem we would have would be the fact that it can't run its battery out anymore thanks to the two S2 engines it ingested from those two Angels."

"And what the hell are we supposed to do if the Eva goes berserk again, huh?" Touji asked from the living room with a glare at the major, "Tell me that. We already had to shoot the damned thing to get it to stop the last time, and now you wanna try talking to it and hope to what God there is that it doesn't go bonkers again?"

Hikari looked back at them, "I'm with Touji on this one. Unit-01 went right after Asuka when it fought against us, what's to stop it this time?" She asked worriedly.

"We have countermeasures in place to keep the Eva in check if it goes berserk, and ways of taking it down without destroying it if necessary," Misato said, having expected some resistance to the idea. "All of you will be on the bridge while we try to make contact with Shinji, and we'll have our anit-Angel restraints put in place to keep the Eva still until we can deliver a powerful enough blow to immobilize it."

"And what happens if we can't make contact?" Mari asked, looking between the two women, "I mean, sure, I wanna know Shinji's okay, but what if we can't hear anything, or he can't?"

"He'll hear us," Yui sad, smiling at the younger girl. "I know I heard everything that went on whenever Shinji or Rei were piloting Unit-01."

=x=

Keel Lorenz was a man of profound patience, and sharp wit, but the wait he had to endure with his latest project against NERV was just driving him mad...er...Unit-13 aside as the most advanced unit even among the M.06 and the newly finished M.09, his latest project would render the piloted units obsolete. The previous designs had lacked many things, imagination among them.

The Evangelion bio-mechs were to be synthetic Angels created to combat Adam's spawn in hopes of prolonging humanities waning hold upon the world. His vision of the future, however, after Instrumentality was achieved and he became the God of the new world he would create for himself, were is own brand of Angels.

When the final battle began, his man-made army would descend upon Tokyo-3 like one of the great plagues of the Bible, and cleanse it of the fools that had opposed him. His fellow members of Seele would, of course, need to be dealt with, but that would be a simple thing...once he had his new body. A body that was now taking shape in the form of a God itself befitting his new rule to come.

The Armos would be his greatest creation. It would be the key to his new world, and he would be the key to the Armos as its soul. Gabriel would surely see it fit to reward him further once his lesser tasks were complete, but he would settle for immortality that would come from his joining with the titanic being that was to be Armos when it was complete.

Right now, however, he had a message to send. A message that would surely send Gendo Ikari into a panicked state. If Unit-13 didn't destroy him first. A smile played across the elder's face in anticipation of what was to come.

Gendo Ikari had committed the sin of treason against his master, as such, his slave would need to be punished...most severely.

=x=

"Is it me, or are there a lot more suits around here today?" Touji asked as he and Hikari walked through the halls of NERV, noting that there was a Section-2 agent every other door.

Hikari nodded nervously, remembering Ritsuko's warning about the men in black suits working for Seele, and being a large threat to them all. "Maybe it's because of what we're doing today?"

Touji shrugged as they passed another black-suited agent. "Dunno, don't care, I just know that these guys give me the creeps," he said, glaring at one of them as the made their way to the bridge, "It's like they're just waiting to blow a gasket."

The doors opened into the command center, revealing Ritsuko, Maya and Aoba getting things set up with Asuka, Mari, Mana, Rei and Kensuke waiting patiently. Misato saw them and smiled, "Oh, great, you guys are just in time."

The large screen in the front of the room flickered to reveal Unit-01 being brought up into the Geo-Front. It looked far bigger than it had once before. The armor was still mostly purple, but the orange high lights had been replaced by some black armaments, as well as more green. It was also thicker than it had been with more restraints in place, for good reasons.

Unit-01, among Evangelions, was now an armored tank.

"Jeez," Kensuke breathed out, "That's Unit-01?"

Ritsuko nodded, "The latest in our F-type developments," she said proudly, "May I present Super Evangelion Unit-01."

Maya almost let out a giggle at the face Aoba pulled at the Unit's new designation and smacked her boyfriend on the shoulder. "Asuka, we're ready for you to try talking to him now."

Asuka sighed as they opened up a video feed to the cockpit, and took a headset from the console, "Okay, but I'm still not sure about this...what do I say?"

"Just talk to him," Ritsuko said, "Call his name, or something to get his attention. We're linked directly to the wave length, so any thought noise that comes from Unit-01 will be displayed here on the screen." She gestured to her the screen left of the one displaying Unit-01.

Asuka nodded and placed the microphone near her lips, "Um...Shinji?" She started out hesitantly, "Shinji, can you hear me?"

"Anything?" Ritsuko asked.

The screen was blank, displaying nothing.

"I don't see any reactions," Hyuuga growled, "Come on, kid, say something!"

Asuka tried again, "Listen, Shinji, if you can hear me, then at least give us a sign." She said, watching the screen, yet nothing happened. Was he really gone? Fear suddenly started to wash over her. this was her one hope of getting through this with her mind intact. They had told her that they would be able to retrieve Shinji from Unit-01, but they had to make contact first...and if they couldn't make contact...

"Shinji, please," Misato looked over at the girl when she spoke again, an unmistakable quaver in her voice, "Please, you have to answer me, or else I won't know what to do!"

Hyuuga looked back at the girl for a moment, seeing not a pilot, but a young girl desperate for what little hope she had left to hold on. Maya bit her lip in sympathy as the girl tried to bring herself back under control.

"You said that you wanted to live through all of this, right?" Asuka said, watching the screen for any sign of reaction, "Remember the dream you told me about? About living in the countryside after this was all over? I want that." She said truthfully, "I want it so badly that I can't stand it, but it's nothing if you're not there with me."

The screen buzzed for a moment, alerting Hyuuga to something very faint, "I have some thought noise," he said quietly, alerting his companions, "Keep going Asuka!"

Asuka nodded, emboldened, "When you asked me to marry you, I was so happy," she admitted, "No one's ever treated me the way you did. Like I was a normal girl instead of a bred and born pilot. All of those times you saw right through me, and made me laugh, I miss that so much!"

The screen began getting static, "I've got him!" Maya shouted, "He can hear you!" She said, beaming.

"Shinji?!" Asuka's voice was filled with such emotion that she could barely contain herself, because a moment later, something happened that would strengthen the resolve of every pilot.

The Evangelion raised its head, and looked right at the camera that was trained on it, and words began appearing on the screen.

 _A...su...ka_

=x=

The command center was in an uproar as the fragmented name of the second in command pilot appeared on the screen, much to Section Two's amusement as the men in black suits quietly entered the room, weapons drawn. The man in the lead aimed his weapon at his preferred target; Gendo Ikari.

But, as it happened, their task would not be so easy to accomplish as the click of a hammer being pulled back alerted the men to a different weapon. "I'm sorry," Ryoji Kaji said from his place behind the Vice-Commander, "But you won't be getting the drop on us today."

The first shot fired, causing the room erupting into chaos.

Hikari and Mana shrieked and ducked under the consoles to avoid the gunfire whilst Kensuke shocked everyone, and barreled right into the nearest gunner, knocking him flat, and swiping his gun from him. Touji was close behind him and grabbed up a fallen pistol, "Hey, Ken, how do I - "

"Pull the back half back to load the chamber!" Kensuke roared over the rapid fire of his weapon, "then pull the trigger, and keep going!"

Rei and Asuka rushed into the fray as well while more men tried to flood into the command center, only to be taken down Kaji and Gendo's shots while Fuyutsuki punched in the codes to lock the doors.

Ritsuko took cover behind Misato as the woman fired her weapon, checking the monitors for the base, "All of the Section Two agents have started attacking NERV personnel! It's a siege!"

"No shit, Sherlock!" Misato shouted as she fired, "Somebody get the kids out of here!"

Kensuke scoffed, and let loose another round from the AK-47 he'd picked up, "Are you kiddin' me! I'm in heave over here!"

Touji nearly laughed as he one of his shot knocked one man to the ground flat on his back where he stayed, "You crazy military nerd," he grinned grimly, "Who'd have thought that shit would come in han - ack!" A bullet grazed his cheek, a crimson flow beginning down his face.

"Touji!" Hikari screamed as she saw her boyfriend stagger back from shock before he fire off another shot,ducking behind a desk for cover. He was fine, more or less, but the blow to his pride hurt almost as much as the bullet wound.

"Stay there!" He roared, ejecting the clip, "Ken, I'm outta ammo!"

Hyuuga tossed him a clip, "Here, standard forty-five caliber," he said as the boy reloaded, and took aim with his own sidearm. Touji nodded his thanks and turned his attention back to the fire fight as Asuka whipped around and roundhoused a man in the neck, snapping it at an awkward angle.

"Hey, Mari, where are you!" The red head snapped, "You've had the same training I've had, you know?!"

Suddenly Mari came out from behind one of the men and slashed him with a knife Asuka never knew the girl carried. Mari just grinned at her, "Sorry I'm late, Princess! I had to find my knife!"

Rei brought another man down in a tight hold with his arm brought behind his back painfully as she relieved him of his weapon and shot the man in the head, throwing the extra magazine he carried to Kensuke. The boy caught it, ejecting the spent clip and reloading a swift movement before he let loose again, taking out what remained of the men that had attacked.

Ryoji replaced an empty clip at his belt, "Well, that was fun...everyone alright?"

"We're okay," Mana said as she and Hikari came out from hiding, the latter rushing over to Touji and fussing over his wound. "What the hell was that all about?"

Gendo snorted while reloading his clips, "A safe bet would be that Seele has order our termination thanks to this latest fiasco." He said and holstered his pistol, looking down at the bespecaled pilot, "that was fine shooting, Kensuke, where did you learn to operate a machine gun?"

Now it was Touji's turn to snort, wincing at the pain it caused his cheek, "You're joking, right, Boss?" He jerked his thumb at his friend, "This guy could probably build one and not even need to see the instruction book!"

Kensuke scratched the back of his head in embarrassment before his eyes landed on Rei, and noticed that she had a red stain on her abdomen, "Oh, shit, Rei - !"

Rei shook her head as he came forward to check her over, "The blood does not belong to me," she stated, smiling at his concern, "You were amazing, Kensuke," she then leaned over and kissed his cheek tenderly.

Gendo groaned, "I'm never going to get used to that...Ritsuko, is there an easy way of getting rid of all of these rats?"

Ritsuko was typing away at her console, her fingers flying across the keys, "All remaining personnel have reached safe rooms, but the Section Two men are swarming all over the place, so it wouldn't be easy to take back the base, at least not without casualties." She said, frowning, "But I think I have a way to do it."

Misato huffed, and placed her hands on her hips, "Then why haven't you done it, yet?" She asked angrily, "In case you haven't noticed, we're in the middle of a war here, Ritsuko!"

"This is why." She said, bringing up the screen again, and showed none other than Unit-01 roaring maddly, and trying to break free of its restraints. "Unit-01, or rather, Shinji, must have heard the gun shots, and now he's trying to get to us."

"So you wanna use Unit-01 to get rid of these guys?" Touji asked, holding onto a trembling Hikari as they heard more gun fire throughout the base.

Ritsuko nodded, "My plan is two fold," she said as she typed, "First thing's first, I'm shutting off any and all exits, that way we won't let any of Seele's goons get away, then I can reroute our supply of LCL into the hallways, and wash those idiots into the lake just outside the base. Next, we convince Unit-01 that they're enemies, and try to get it to deal with them much quicker than we could."

Mari gave the woman a look, "How do you convince an Eva to do anything outside of a pilot's will?"

The blonde looked at her, "I'll be leaving that to Asuka."

Asuka grinned maliciously, "I'm sure he'll forgive me for this," she said and grabbed the headset again, "Shinji...I need you to do something for me, okay?" The Eva stopped its struggling, and raised its head again, "Okay, that's good, now listen. Some really bad men were attacking us, do you understand?" She said, hoping that he could understand her plea.

She watched the screen, and saw the response being broadcast to them.

 _I understand._

Asuka sighed in relief, "Good, because Ritsuko is going to flush those idiots into the lake, and we need you to handle them for us." She said, looking behind her at the bodies, some of which were being looked by Kensuke looking for anything he could add to his new arsenal. "Can you do that for us?"

 _I will._

Asuka nodded, smiling, "Alright, we're gonna have the doctor get those restraints off of you, and then you can go to town on these goons," she said, giving the doctor a pointed look. "Just don't try to destroy anything, okay?"

The Evangelion nodded its head, and the restraining bolts were loosed.

"Flooding the halls now," Aoba said, "Is it wrong that I kind of feel sorry for these guys?"

Hikari, near hysterics, glared at the man, "They just tried to kill us!"

"Sorry."

In front of the base, a hatch opened up as a torrent of the orange liquid rushed from the opening, spilling into the lake with dozens of Seele's agents along with it. As they tried to make for the shoreline, Unit-01 beat them to the punch. Its eyes were glowing dangerously, and Asuka knew exactly what was about to happen. "Hang on to something!"

A moment later, the eyes of the behemoth flashed, and a gigantic cross erupted from the lake, incinerating anything caught within the blast. Asuka shuddered as she looked back up at the monitor, seeing that there was no water left, nor was there any sign of the Section Two agents.

"Asuka," Gendo intoned, causing the girl to look at him, "Try to coax Unit-01 back into the elevator, and to sleep, we'll see if can't make a stronger connection to Shinji later. But right now, we need to be better prepared for another attack like this."

* * *

 _ **Unit-01 has been reborn. Seele has attacked NERV, and NERV has fought back. What's going to happen from this point? Keep reading to find out, and don't forget to review!**_


End file.
